In this work, filament-based 3D-printing, the most widely used sub-category of material extrusion additive manufacturing (MEAM), is presented as a promising manufacturing platform for the production of subcutaneous implants. Print nozzle diameters as small as 100 µm were utilized demonstrating MEAM of advanced porous internal structures at the given cylindrical implant geometry of 2 mm × 40 mm. The bottlenecks related to high-resolution MEAM of subcutaneous implants are systematically analyzed and the print process is optimized accordingly. Custom synthesized biodegradable phase-separated poly(ether ester) multiblock copolymers exhibiting appropriate melt viscosity at comparatively low printing temperatures of 135 °C and 165 °C were utilized as 3D-printing feedstock. The print process was optimized to minimize thermomechanical polymer degradation by employing print speeds of 30 mm∙s−1 in combination with a nozzle diameter of 150 µm at layer heights of 110 µm. These results portray the basis for further development of subcutaneous implantable drug delivery systems where drug release profiles can be tailored through the adaption of the internal implant structure, which cannot be achieved using existing manufacturing techniques.